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Calcium in PDB 2y4v: Crystal Structure of Human Calmodulin in Complex with A Dap Kinase-1 Mutant (W305Y) Peptide

Enzymatic activity of Crystal Structure of Human Calmodulin in Complex with A Dap Kinase-1 Mutant (W305Y) Peptide

All present enzymatic activity of Crystal Structure of Human Calmodulin in Complex with A Dap Kinase-1 Mutant (W305Y) Peptide:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of Human Calmodulin in Complex with A Dap Kinase-1 Mutant (W305Y) Peptide, PDB code: 2y4v was solved by I.De Diego, F.Lehmann, M.Wilmanns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.20 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 65.561, 33.923, 74.257, 90.00, 92.21, 90.00
R / Rfree (%) 22.908 / 23.825

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Calmodulin in Complex with A Dap Kinase-1 Mutant (W305Y) Peptide (pdb code 2y4v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human Calmodulin in Complex with A Dap Kinase-1 Mutant (W305Y) Peptide, PDB code: 2y4v:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2y4v

Go back to Calcium Binding Sites List in 2y4v
Calcium binding site 1 out of 4 in the Crystal Structure of Human Calmodulin in Complex with A Dap Kinase-1 Mutant (W305Y) Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Calmodulin in Complex with A Dap Kinase-1 Mutant (W305Y) Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1150

b:25.8
occ:1.00
 O A:HOH2153 1.8 36.2 1.0
OD1 A:ASP130 2.0 32.7 1.0
O A:GLN136 2.3 29.6 1.0
OD1 A:ASP132 2.4 44.9 1.0
OE2 A:GLU141 2.4 41.1 1.0
OE1 A:GLU141 2.5 34.3 1.0
OD1 A:ASP134 2.5 35.2 1.0
CD A:GLU141 2.8 36.8 1.0
CG A:ASP130 3.2 36.0 1.0
CG A:ASP134 3.5 34.3 1.0
C A:GLN136 3.5 29.6 1.0
CG A:ASP132 3.5 47.2 1.0
OD2 A:ASP134 4.0 35.3 1.0
CA A:ASP130 4.0 40.5 1.0
OD2 A:ASP132 4.0 49.8 1.0
OD2 A:ASP130 4.0 36.6 1.0
CB A:ASP130 4.1 39.8 1.0
N A:GLN136 4.1 30.8 1.0
N A:ASP132 4.2 48.2 1.0
N A:ILE131 4.3 45.5 1.0
N A:ASP134 4.3 38.2 1.0
CA A:GLN136 4.3 29.2 1.0
CG A:GLU141 4.4 35.8 1.0
O A:HOH2145 4.4 40.5 1.0
N A:VAL137 4.4 28.3 1.0
CA A:VAL137 4.4 28.1 1.0
C A:ASP130 4.5 44.0 1.0
CB A:ASP134 4.6 36.7 1.0
N A:GLY133 4.6 43.7 1.0
N A:ASN138 4.6 30.3 1.0
CB A:ASP132 4.7 48.7 1.0
CB A:GLN136 4.8 28.3 1.0
CA A:ASP134 4.8 35.9 1.0
CA A:ASP132 4.8 48.4 1.0
N A:GLY135 4.9 33.1 1.0
O A:HOH2154 4.9 54.1 1.0
C A:ASP132 5.0 47.3 1.0
C A:VAL137 5.0 28.6 1.0

Calcium binding site 2 out of 4 in 2y4v

Go back to Calcium Binding Sites List in 2y4v
Calcium binding site 2 out of 4 in the Crystal Structure of Human Calmodulin in Complex with A Dap Kinase-1 Mutant (W305Y) Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Calmodulin in Complex with A Dap Kinase-1 Mutant (W305Y) Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1151

b:22.0
occ:1.00
 OD1 A:ASP21 2.3 28.8 1.0
O A:THR27 2.4 29.9 1.0
OD1 A:ASP25 2.4 34.1 1.0
O A:HOH2031 2.4 31.4 1.0
OE1 A:GLU32 2.4 26.5 1.0
OD1 A:ASP23 2.5 34.5 1.0
OE2 A:GLU32 2.6 31.4 1.0
CD A:GLU32 2.8 27.3 1.0
CG A:ASP25 3.3 37.4 1.0
CG A:ASP23 3.4 38.0 1.0
CG A:ASP21 3.4 30.5 1.0
C A:THR27 3.6 27.6 1.0
OG1 A:THR27 3.8 36.3 1.0
OD2 A:ASP23 3.8 38.6 1.0
OD2 A:ASP25 3.9 40.6 1.0
N A:THR27 4.1 29.6 1.0
CA A:ASP21 4.2 26.3 1.0
CB A:ASP21 4.2 25.9 1.0
N A:ASP25 4.3 34.7 1.0
OD2 A:ASP21 4.3 27.6 1.0
CG A:GLU32 4.3 29.9 1.0
CA A:THR27 4.4 29.1 1.0
CB A:ASP25 4.4 36.2 1.0
N A:ASP23 4.4 32.6 1.0
N A:ILE28 4.5 24.8 1.0
C A:ASP21 4.5 27.7 1.0
CA A:ILE28 4.6 22.3 1.0
CB A:ASP23 4.6 35.7 1.0
O A:HOH2037 4.6 31.8 1.0
CA A:ASP25 4.7 35.5 1.0
CB A:THR27 4.7 31.9 1.0
N A:LYS22 4.8 28.3 1.0
CA A:ASP23 4.8 35.0 1.0
N A:GLY26 4.8 31.6 1.0
O A:HOH2041 4.9 38.5 1.0
N A:GLY24 4.9 34.1 1.0
C A:ASP23 4.9 35.5 1.0
C A:ASP25 4.9 34.3 1.0
CG2 A:THR29 5.0 29.4 1.0
N A:THR29 5.0 24.7 1.0

Calcium binding site 3 out of 4 in 2y4v

Go back to Calcium Binding Sites List in 2y4v
Calcium binding site 3 out of 4 in the Crystal Structure of Human Calmodulin in Complex with A Dap Kinase-1 Mutant (W305Y) Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Calmodulin in Complex with A Dap Kinase-1 Mutant (W305Y) Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1152

b:18.3
occ:1.00
 OD1 A:ASP57 2.3 26.2 1.0
OD1 A:ASN61 2.3 31.5 1.0
OE1 A:GLU68 2.3 20.6 1.0
O A:THR63 2.4 24.4 1.0
O A:HOH2095 2.4 30.5 1.0
OD1 A:ASP59 2.5 34.6 1.0
OE2 A:GLU68 2.7 19.3 1.0
CD A:GLU68 2.8 16.9 1.0
CG A:ASN61 3.4 32.5 1.0
O A:HOH2094 3.4 44.6 1.0
CG A:ASP59 3.4 34.4 1.0
CG A:ASP57 3.5 30.2 1.0
C A:THR63 3.6 22.3 1.0
OD2 A:ASP59 3.7 35.9 1.0
ND2 A:ASN61 4.0 34.0 1.0
N A:THR63 4.2 26.2 1.0
OD2 A:ASP57 4.3 29.1 1.0
CG A:GLU68 4.3 17.1 1.0
N A:ASN61 4.3 33.7 1.0
CA A:ASP57 4.3 28.0 1.0
CB A:ASP57 4.4 26.8 1.0
N A:ASP65 4.4 21.4 1.0
N A:ILE64 4.5 23.0 1.0
N A:ASP59 4.5 33.0 1.0
CB A:ASN61 4.5 34.0 1.0
CA A:ILE64 4.5 20.3 1.0
CA A:THR63 4.5 25.0 1.0
OD2 A:ASP65 4.6 34.0 1.0
OG1 A:THR63 4.7 27.3 1.0
C A:ASP57 4.7 28.6 1.0
CB A:ASP59 4.7 35.4 1.0
N A:GLY62 4.7 31.2 1.0
CG A:ASP65 4.8 25.5 1.0
CA A:ASN61 4.8 33.8 1.0
C A:ILE64 4.8 22.7 1.0
O A:HOH2097 4.8 32.2 1.0
N A:GLY60 4.9 34.8 1.0
N A:ALA58 4.9 28.4 1.0
CA A:ASP59 4.9 33.8 1.0
C A:ASN61 5.0 33.9 1.0

Calcium binding site 4 out of 4 in 2y4v

Go back to Calcium Binding Sites List in 2y4v
Calcium binding site 4 out of 4 in the Crystal Structure of Human Calmodulin in Complex with A Dap Kinase-1 Mutant (W305Y) Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Calmodulin in Complex with A Dap Kinase-1 Mutant (W305Y) Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1153

b:22.4
occ:1.00
 OD1 A:ASP94 2.3 32.7 1.0
O A:TYR100 2.3 25.8 1.0
O A:HOH2113 2.3 30.1 1.0
OE1 A:GLU105 2.4 29.2 1.0
OD1 A:ASN98 2.4 28.9 1.0
OD1 A:ASP96 2.5 40.2 1.0
OE2 A:GLU105 2.5 29.3 1.0
CD A:GLU105 2.8 28.0 1.0
CG A:ASP96 3.3 42.0 1.0
CG A:ASN98 3.5 34.0 1.0
C A:TYR100 3.5 26.1 1.0
CG A:ASP94 3.5 34.1 1.0
OD2 A:ASP96 3.7 43.6 1.0
N A:TYR100 4.0 30.3 1.0
ND2 A:ASN98 4.2 33.8 1.0
N A:ASN98 4.2 38.1 1.0
CG A:GLU105 4.3 27.2 1.0
CA A:ASP94 4.3 34.0 1.0
OD2 A:ASP94 4.3 36.4 1.0
N A:ASP96 4.4 41.0 1.0
CA A:TYR100 4.4 27.6 1.0
CB A:ASP94 4.5 33.8 1.0
O A:HOH2148 4.5 31.9 1.0
N A:ILE101 4.5 23.7 1.0
CB A:ASN98 4.5 37.2 1.0
CA A:ILE101 4.5 22.9 1.0
C A:ASP94 4.5 35.2 1.0
N A:SER102 4.5 23.4 1.0
CB A:ASP96 4.5 42.5 1.0
N A:GLY97 4.5 40.2 1.0
CA A:ASN98 4.7 37.5 1.0
N A:LYS95 4.8 36.4 1.0
CB A:TYR100 4.8 27.4 1.0
CA A:ASP96 4.8 41.9 1.0
C A:ASP96 4.9 42.3 1.0
O A:ASP94 4.9 37.2 1.0
C A:ILE101 5.0 23.2 1.0
CA A:GLY99 5.0 35.1 1.0

Reference:

I.De Diego, J.Kuper, F.Lehmann, M.Wilmanns. A Journey Through the Dap Kinase Architecture To Be Published.
Page generated: Tue Jul 8 09:32:13 2025

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